Paul Bertone

Paul Bertone

Research Group Leader

PhD Yale University, 2005. At EMBL–EBI since 2005. Joint appointments in Genome Biology and Developmental Biology Units. Associate Investigator, Wellcome Trust – Medical Research Council Stem Cell Institute, University of Cambridge.

ORCID iD: 0000-0001-5059-4829

Tel:+44 (0)1223 492 540 / Fax:+44 (0)1223 494 468

Research

Find out about research activity in the Bertone research group

Publications

2014

Citrullination regulates pluripotency and histone H1 binding to chromatin.
Christophorou MA, Castelo-Branco G, Halley-Stott RP, Oliveira CS, Loos R, Radzisheuskaya A, Mowen KA, Bertone P, Silva JC, Zernicka-Goetz M, Nielsen ML, Gurdon JB, Kouzarides T.
Nature Volume 507 (2014) p.104-108
DOI: 10.1038/nature12942

The ability of inner-cell-mass cells to self-renew as embryonic stem cells is acquired following epiblast specification.
Boroviak T, Loos R, Bertone P, Smith A, Nichols J.
Nat Cell Biol Volume 16 (2014) p.516-528
DOI: 10.1038/ncb2965

2013

The non-coding snRNA 7SK controls transcriptional termination, poising, and bidirectionality in embryonic stem cells.
Castelo-Branco G, Amaral PP, Engström PG, Robson SC, Marques SC, Bertone P, Kouzarides T.
Genome Biol Volume 14 (2013) p.r98
DOI: 10.1186/gb-2013-14-9-r98

A high-content small molecule screen identifies sensitivity of glioblastoma stem cells to inhibition of polo-like kinase 1.
Danovi D, Folarin A, Gogolok S, Ender C, Elbatsh AM, Engström PG, Stricker SH, Gagrica S, Georgian A, Yu D, U KP, Harvey KJ, Ferretti P, Paddison PJ, Preston JE, Abbott NJ, Bertone P, Smith A, Pollard SM.
PLoS One Volume 8 (2013) p.e77053
DOI: 10.1371/journal.pone.0077053

Systematic evaluation of spliced alignment programs for RNA-seq data.
Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P, RGASP Consortium.
Nat Methods Volume 10 (2013) p.1185-1191
DOI: 10.1038/nmeth.2722

Towards practical, high-capacity, low-maintenance information storage in synthesized DNA.
Goldman N, Bertone P, Chen S, Dessimoz C, LeProust EM, Sipos B, Birney E.
Nature Volume 494 (2013) p.77-80
DOI: 10.1038/nature11875

Assessment of transcript reconstruction methods for RNA-seq.
Steijger T, Abril JF, Engström PG, Kokocinski F, Hubbard TJ, Guigó R, Harrow J, Bertone P, RGASP Consortium.
Nat Methods Volume 10 (2013) p.1177-1184
DOI: 10.1038/nmeth.2714

Identification of the missing pluripotency mediator downstream of leukaemia inhibitory factor.
Martello G, Bertone P, Smith A.
EMBO J Volume 32 (2013) p.2561-2574
DOI: 10.1038/emboj.2013.177

SMIM1 underlies the Vel blood group and influences red blood cell traits.
Cvejic A, Haer-Wigman L, Stephens JC, Kostadima M, Smethurst PA, Frontini M, van den Akker E, Bertone P, Bielczyk-Maczyńska E, Farrow S, Fehrmann RS, Gray A, de Haas M, Haver VG, Jordan G, Karjalainen J, Kerstens HH, Kiddle G, Lloyd-Jones H, Needs M, Poole J, Soussan AA, Rendon A, Rieneck K, Sambrook JG, Schepers H, Silljé HH, Sipos B, Swinkels D, Tamuri AU, Verweij N, Watkins NA, Westra HJ, Stemple D, Franke L, Soranzo N, Stunnenberg HG, Goldman N, van der Harst P, van der Schoot CE, Ouwehand WH, Albers CA.
Nat Genet Volume 45 (2013) p.542-545
DOI: 10.1038/ng.2603

2012

Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival.
Engström PG, Tommei D, Stricker SH, Ender C, Pollard SM, Bertone P.
Genome Med Volume 4 (2012) p.76
DOI: 10.1186/gm377

NuRD suppresses pluripotency gene expression to promote transcriptional heterogeneity and lineage commitment.
Reynolds N, Latos P, Hynes-Allen A, Loos R, Leaford D, O'Shaughnessy A, Mosaku O, Signolet J, Brennecke P, Kalkan T, Costello I, Humphreys P, Mansfield W, Nakagawa K, Strouboulis J, Behrens A, Bertone P, Hendrich B.
Cell Stem Cell Volume 10 (2012) p.583-594
DOI: 10.1016/j.stem.2012.02.020

NuRD-mediated deacetylation of H3K27 facilitates recruitment of Polycomb Repressive Complex 2 to direct gene repression.
Reynolds N, Salmon-Divon M, Dvinge H, Hynes-Allen A, Balasooriya G, Leaford D, Behrens A, Bertone P, Hendrich B.
EMBO J Volume 31 (2012) p.593-605
DOI: 10.1038/emboj.2011.431

Genome-wide characterization of Foxa2 targets reveals upregulation of floor plate genes and repression of ventrolateral genes in midbrain dopaminergic progenitors.
Metzakopian E, Lin W, Salmon-Divon M, Dvinge H, Andersson E, Ericson J, Perlmann T, Whitsett JA, Bertone P, Ang SL.
Development Volume 139 (2012) p.2625-2634
DOI: 10.1242/dev.081034

Compound inheritance of a low-frequency regulatory SNP and a rare null mutation in exon-junction complex subunit RBM8A causes TAR syndrome.
Albers CA, Paul DS, Schulze H, Freson K, Stephens JC, Smethurst PA, Jolley JD, Cvejic A, Kostadima M, Bertone P, Breuning MH, Debili N, Deloukas P, Favier R, Fiedler J, Hobbs CM, Huang N, Hurles ME, Kiddle G, Krapels I, Nurden P, Ruivenkamp CA, Sambrook JG, Smith K, Stemple DL, Strauss G, Thys C, van Geet C, Newbury-Ecob R, Ouwehand WH, Ghevaert C.
Nat Genet Volume 44 (2012) p.435-9, s1-2
DOI: 10.1038/ng.1083

2011

Exome sequencing identifies NBEAL2 as the causative gene for gray platelet syndrome.
Albers CA, Cvejic A, Favier R, Bouwmans EE, Alessi MC, Bertone P, Jordan G, Kettleborough RN, Kiddle G, Kostadima M, Read RJ, Sipos B, Sivapalaratnam S, Smethurst PA, Stephens J, Voss K, Nurden A, Rendon A, Nurden P, Ouwehand WH.
Nat Genet Volume 43 (2011) p.735-737
DOI: 10.1038/ng.885

2010

PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci.
Salmon-Divon M, Dvinge H, Tammoja K, Bertone P.
BMC Bioinformatics Volume 11 (2010) p.415
DOI: 10.1186/1471-2105-11-415

Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression.
Git A, Dvinge H, Salmon-Divon M, Osborne M, Kutter C, Hadfield J, Bertone P, Caldas C.
RNA Volume 16 (2010) p.991-1006
DOI: 10.1261/rna.1947110

2009

GLOBAL ANALYSIS OF PROTEIN ACTIVITY USING PROTEOME CHIPS
SNYDER MICHAEL, ZHU HENG, BERTONE PAUL, BIDLINGMAIER SCOTT M, BILGIN METIN, CASAMAYOR ANTONIO J, GERSTEIN MARK, JANSEN RONALD, LAN NING.
Volume (2009) p.

HTqPCR: high-throughput analysis and visualization of quantitative real-time PCR data in R.
Dvinge H, Bertone P.
Bioinformatics Volume 25 (2009) p.3325-3326
DOI: 10.1093/bioinformatics/btp578

Mapping organelle proteins and protein complexes in Drosophila melanogaster.
Tan DJ, Dvinge H, Christoforou A, Bertone P, Martinez Arias A, Lilley KS.
J Proteome Res Volume 8 (2009) p.2667-2678
DOI: 10.1021/pr800866n

2008

Modeling of C/EBPalpha mutant acute myeloid leukemia reveals a common expression signature of committed myeloid leukemia-initiating cells.
Kirstetter P, Schuster MB, Bereshchenko O, Moore S, Dvinge H, Kurz E, Theilgaard-Mönch K, Månsson R, Pedersen TA, Pabst T, Schrock E, Porse BT, Jacobsen SE, Bertone P, Tenen DG, Nerlov C.
Cancer Cell Volume 13 (2008) p.299-310
DOI: 10.1016/j.ccr.2008.02.008

Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila.
Kind J, Vaquerizas JM, Gebhardt P, Gentzel M, Luscombe NM, Bertone P, Akhtar A.
Cell Volume 133 (2008) p.813-828
DOI: 10.1016/j.cell.2008.04.036

2006

Transcriptional regulatory networks in bacteria: from input signals to output responses.
Seshasayee AS, Bertone P, Fraser GM, Luscombe NM.
Curr Opin Microbiol Volume 9 (2006) p.511-519
DOI: 10.1016/j.mib.2006.08.007

Target hub proteins serve as master regulators of development in yeast.
Borneman AR, Leigh-Bell JA, Yu H, Bertone P, Gerstein M, Snyder M.
Genes Dev Volume 20 (2006) p.435-448
DOI: 10.1101/gad.1389306

Design optimization methods for genomic DNA tiling arrays.
Bertone P, Trifonov V, Rozowsky JS, Schubert F, Emanuelsson O, Karro J, Kao MY, Snyder M, Gerstein M.
Genome Res Volume 16 (2006) p.271-281
DOI: 10.1101/gr.4452906

2005

Global changes in STAT target selection and transcription regulation upon interferon treatments.
Hartman SE, Bertone P, Nath AK, Royce TE, Gerstein M, Weissman S, Snyder M.
Genes Dev Volume 19 (2005) p.2953-2968
DOI: 10.1101/gad.1371305

Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping.
Royce TE, Rozowsky JS, Bertone P, Samanta M, Stolc V, Weissman S, Snyder M, Gerstein M.
Trends Genet Volume 21 (2005) p.466-475
DOI: 10.1016/j.tig.2005.06.007

Prospects and challenges in proteomics.
Bertone P, Snyder M.
Plant Physiol Volume 138 (2005) p.560-562
DOI: 10.1104/pp.104.900154

Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles.
Gilad Y, Rifkin SA, Bertone P, Gerstein M, White KP.
Genome Res Volume 15 (2005) p.674-680
DOI: 10.1101/gr.3335705

Advances in functional protein microarray technology.
Bertone P, Snyder M.
FEBS J Volume 272 (2005) p.5400-5411
DOI: 10.1111/j.1742-4658.2005.04970.x

Global analysis of protein activities using proteome chips
SNYDER MICHAEL, ZHU HENGZHU, BERTONE PAUL, BIDLINGMAIER SCOTT M, BILGIN METIN, CASAMAYOR ANTONIO, GERSTEIN MARK, JANSEN RONALD, LAN NING.
Volume (2005) p.

2004

Global identification of human transcribed sequences with genome tiling arrays.
Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL, Tongprasit W, Samanta M, Weissman S, Gerstein M, Snyder M.
Science Volume 306 (2004) p.2242-2246
DOI: 10.1126/science.1103388

CREB binds to multiple loci on human chromosome 22.
Euskirchen G, Royce TE, Bertone P, Martone R, Rinn JL, Nelson FK, Sayward F, Luscombe NM, Miller P, Gerstein M, Weissman S, Snyder M.
Mol Cell Biol Volume 24 (2004) p.3804-3814
DOI: 10.1128/mcb.24.9.3804-3814.2004

The ENCODE (ENCyclopedia Of DNA Elements) Project.
ENCODE Project Consortium.
Science Volume 306 (2004) p.636-640
DOI: 10.1126/science.1105136

Fast optimal genome tiling with applications to microarray design and homology search.
Berman P, Bertone P, Dasgupta B, Gerstein M, Kao MY, Snyder M.
J Comput Biol Volume 11 (2004) p.766-785
DOI: 10.1089/cmb.2004.11.766

2003

ExpressYourself: A modular platform for processing and visualizing microarray data.
Luscombe NM, Royce TE, Bertone P, Echols N, Horak CE, Chang JT, Snyder M, Gerstein M.
Nucleic Acids Res Volume 31 (2003) p.3477-3482
DOI: 10.1093/nar/gkg628

The transcriptional activity of human Chromosome 22.
Rinn JL, Euskirchen G, Bertone P, Martone R, Luscombe NM, Hartman S, Harrison PM, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M.
Genes Dev Volume 17 (2003) p.529-540
DOI: 10.1101/gad.1055203

Distribution of NF-kappaB-binding sites across human chromosome 22.
Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NM, Rinn JL, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M.
Proc Natl Acad Sci U S A Volume 100 (2003) p.12247-12252
DOI: 10.1073/pnas.2135255100

SPINE 2: a system for collaborative structural proteomics within a federated database framework.
Goh CS, Lan N, Echols N, Douglas SM, Milburn D, Bertone P, Xiao R, Ma LC, Zheng D, Wunderlich Z, Acton T, Montelione GT, Gerstein M.
Nucleic Acids Res Volume 31 (2003) p.2833-2838
DOI: 10.1093/nar/gkg397

Identification of pseudogenes in the Drosophila melanogaster genome.
Harrison PM, Milburn D, Zhang Z, Bertone P, Gerstein M.
Nucleic Acids Res Volume 31 (2003) p.1033-1037
DOI: 10.1093/nar/gkg169

2002

SNPs on human chromosomes 21 and 22 -- analysis in terms of protein features and pseudogenes.
Balasubramanian S, Harrison P, Hegyi H, Bertone P, Luscombe N, Echols N, McGarvey P, Zhang Z, Gerstein M.
Pharmacogenomics Volume 3 (2002) p.393-402
DOI: 10.1517/14622416.3.3.393

An integrated approach for finding overlooked genes in yeast.
Kumar A, Harrison PM, Cheung KH, Lan N, Echols N, Bertone P, Miller P, Gerstein MB, Snyder M.
Nat Biotechnol Volume 20 (2002) p.58-63
DOI: 10.1038/nbt0102-58

Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae.
Horak CE, Luscombe NM, Qian J, Bertone P, Piccirrillo S, Gerstein M, Snyder M.
Genes Dev Volume 16 (2002) p.3017-3033
DOI: 10.1101/gad.1039602

Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22.
Harrison PM, Hegyi H, Balasubramanian S, Luscombe NM, Bertone P, Echols N, Johnson T, Gerstein M.
Genome Res Volume 12 (2002) p.272-280
DOI: 10.1101/gr.207102

2001

Integrative data mining: the new direction in bioinformatics.
Bertone P, Gerstein M.
IEEE Eng Med Biol Mag Volume 20 (2001) p.33-40
DOI: 10.1109/51.940042

Global analysis of protein activities using proteome chips.
Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, Lan N, Jansen R, Bidlingmaier S, Houfek T, Mitchell T, Miller P, Dean RA, Gerstein M, Snyder M.
Science Volume 293 (2001) p.2101-2105
DOI: 10.1126/science.1062191

2000

Analysis of yeast protein kinases using protein chips.
Zhu H, Klemic JF, Chang S, Bertone P, Casamayor A, Klemic KG, Smith D, Gerstein M, Reed MA, Snyder M.
Nat Genet Volume 26 (2000) p.283-289
DOI: 10.1038/81576